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YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

Genomics, Proteomics & Bioinformatics 2015年第1期13卷 25-35页

作者： Christopher M.Colangelo Mark Shifman Kei-Hoi Cheung Kathryn L.Stone nicholas j.carriero Erol E.Gulcicek TuKiet T.Lam Terence Wu Robert D.Bjornson Can Bruce Angus C.Nairn jesse Rinehart Perry L.Miller Kenneth R.Williams W.M.Keck Foundation Biotechnology Resource Laboratory School of Medicine Yale University Department of Molecular Biophysics & Biochemistry Yale University Yale Center for Medical Informatics School of Medicine Yale University Department of Anesthesiology School of Medicine Yale University Department of Emergency Medicine School of Medicine Yale University VA Connecticut Healthcare System W.M. Keck Foundation Biotechnology Resource Laboratory School of Medicine Yale University Department of Computer Science Yale University Yale Center for Genome Analysis West Campus Yale University Yale West Campus Analytical Core West Campus Yale University Yale Bioinformatics Resource School of Medicine Yale University Department of Psychiatry School of Medicine Yale University Department of Cellular & Molecular Physiology School of Medicine Yale University Systems Biology Institute Yale University

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database（YPED） that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry（LC–MS/MS） database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring（MRM）/selective reaction monitoring（SRM） assay development. We have linked YPED＇s database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.

关键词： Proteomics Database Bioinformatics Mass spectrometry Repository Spectral library

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Classical bovine spongiform encephalopathy and chronic wasting disease:two sides of the prion coin

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Animal Diseases 2024年第1期4卷 1-18页

作者： nicholas j.Haley juergen A.Richt Department of Microbiology and Immunology College of Graduate StudiesMidwestern UniversityGlendaleAZUSA Department of Diagnostic Medicine/Pathobiology College of Veterinary MedicineKansas State UniversityManhattanKSUSA

Transmissible spongiform encephalopathies(TSEs)are a group of progressive and ultimately fatal neurologic diseases of man and animals,all resulting from the propagated misfolding of the host's normal cellular prion protein.These diseases can be spontaneous,heritable,anthropogenic/iatrogenic,or in some cases horizontally transmissible,and include such notable TSEs as bovine spongiform encephalopathy(BSE)of cattle and chronic wasting disease(CWD)of cervids.Although they are both unequivocally protein misfolding disorders,they differ markedly in their pathogenesis,transmissibility,and zoonotic potential.While the BSE epidemic has largely abated over the past three decades following global feed bans on ruminant meat and bone meal,CWD,which is readily transmitted through various forms of excreta,has rapidly expanded from its original endemic zone to encompass much of North America,along with recently identified foci in Scandinavia.Most importantly,although the classical form of BSE has proven transmissible to humans consuming contaminated beef or beef products,so far there have been no conclusive reports on the zoonotic transmission of cWD to humans.The underlying basis for these differences-whether host or agent directed-are not well understood,though may be due to inherent differences in the three-dimensional structure of the misfolded BSE or CWD prion proteins or the expression levels and tissue distribution of respective cellular prion proteins.With the uncontrolled geographic spread of CWD,it is imperative that we improve our understanding of the factors governing prion disease pathogenesis,transmission,and zoonotic potential.

关键词： Prion Bovine Spongiform Encephalopathy Chronic Wasting Disease Transmission Pathogenesis Zoonosis

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HDPairFinder:A data processing platform for hydrogen/deuterium isotopic labeling-based nontargeted analysis of trace-level amino-containing chemicals in environmental water

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journal of Environmental Sciences 2024年第2期136卷 583-593页

作者： Tingting Zhao Kristin Carroll Caley B.Craven nicholas j.P.Wawryk Shipei Xing jian Guo Xing-Fang Li Tao Huan Department of Chemistry Faculty of ScienceUniversity of British ColumbiaVancouver Campus2036 Main MallVancouverBritish ColumbiaV6T 1Z1Canada Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlberta T6G 2G3Canada

The combination of hydrogen/deuterium(H/D)formaldehyde-based isotopic methyl labeling with solid-phase extraction and high-performance liquid chromatography–high resolution mass spectrometry(HPLC-HRMS)is a powerful analytical solution for nontargeted analysis of trace-level amino-containing chemicals in water samples.Given the huge amount of chemical information generated in HPLC-HRMS analysis,identifying all possible H/Dlabeled amino chemicals presents a significant challenge in data processing.To address this,we designed a streamlined data processing pipeline that can automatically extract H/D-labeled amino chemicals from the raw HPLC-HRMS data with high accuracy and efficiency.First,we developed a cross-correlation algorithm to correct the retention time shift resulting from deuterium isotopic effects,which enables reliable pairing of H-and D-labeled peaks.Second,we implemented several bioinformatic solutions to remove false chemical features generated by in-source fragmentation,salt adduction,and natural13C isotopes.Third,we used a data mining strategy to construct the AMINES library that consists of over 38,000 structure-disjointed primary and secondary amines to facilitate putative compound annotation.Finally,we integrated these modules into a freely available R program,HDPairFinder.R.The rationale of each module was justified and its performance tested using experimental H/D-labeled chemical standards and authentic water samples.We further demonstrated the application of HDPairFinder to effectively extract N-containing contaminants,thus enabling the monitoring of changes of primary and secondary N-compounds in authentic water samples.HDPairFinder is a reliable bioinformatic tool for rapid processing of H/D isotopic methyl labeling-based nontargeted analysis of water samples,and will facilitate a better understanding of N-containing chemical compounds in water.

关键词： Isotope labeling Nontargeted analysis Reactive N-compounds HPLC-HRMS Source water

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Considerations for the use of porcine organ donation models in preclinical organ donor intervention research

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Animal Models and Experimental Medicine 2024年第3期7卷 283-296页

作者： Frazer I.Heinis Shaheed Merani nicholas W.Markin Kim F.Duncan Michael j.Moulton Lance Fristoe William E.Thorell Raechel A.Sherrick Tami R.Wells Matthew T.Andrews Marian Urban School of Natural Resources Institute of Agriculture and Natural ResourcesUniversity of Nebraska-LincolnLincolnNebraskaUSA Division of Transplantation and Vascular Surgery Department of SurgeryUniversity of Nebraska Medical CenterOmahaNebraskaUSA Department of Anesthesiology University of Nebraska Medical CenterOmahaNebraskaUSA Division of Cardiothoracic Surgery Department of SurgeryUniversity of Nebraska Medical CenterOmahaNebraskaUSA Clinical Perfusion Nebraska Medicine-Nebraska Medical CenterOmahaNebraskaUSA Department of Neurosurgery University of Nebraska Medical CenterOmahaNebraskaUSA Nutrition and Health Sciences College of Education and Human SciencesUniversity of Nebraska-LincolnLincolnNebraskaUSA Department of Comparative Medicine University of Nebraska Medical CenterOmahaNebraskaUSA

Use of animal models in preclinical transplant research is essential to the optimization of human allografts for clinical transplantation.Animal models of organ donation and preservation help to advance and improve technical elements of solid organ recovery and facilitate research of ischemia-reperfusion injury,organ preservation strategies,and future donor-based interventions.Important considerations include cost,public opinion regarding the conduct of animal research,translational value,and relevance of the animal model for clinical practice.We present an overview of two porcine models of organ donation:donation following brain death(DBD)and donation following circulatory death(DCD).The cardiovascular anatomy and physiology of pigs closely resembles those of humans,making this species the most appropriate for pre-clinical research.Pigs are also considered a potential source of organs for human heart and kidney xenotransplantation.It is imperative to minimize animal loss during procedures that are surgically complex.We present our experience with these models and describe in detail the use cases,procedural approach,challenges,alternatives,and limitations of each model.

关键词： animal model brain death circulatory death organ transplantation

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Breaking the biotrophic interfacial complex:How genome editing can lead to rice blast resistance

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Molecular Plant 2023年第8期16卷 1243-1245页

作者： Vincent Were nicholas j.Talbot The Sainsbury Laboratory University of East AngliaNorwich Research ParkNorwich NR47UHUK

Genome editing is a transformational technology—by precisely altering the coding or regulatory sequence of a specific gene,it is now possible to change specific traits within a wide variety of organisms.As a consequence,plant breeding can be taken to a new level of precision,and many countries are moving rapidly to adopt new legislation to permit genome editing(Greenwood et al.,2023).However,genome editing has so far seldom been used to develop disease-resistant crops.This is because plant immunity often depends on single dominant resistance genes,which encode immune receptors that recognize secreted effectors deployed by plant pathogens(jones and Dangl,2006).In this context,genetic modification has proven to be a much more powerful technology so far to introduce these genes from distinct varieties,or even different species,to develop disease resistant crop species(Greenwood et al.,2023),especially when multiple disease-resistance loci can be introduced together to provide more durable resistance(Luo et al.,2021).Genome editing can be used in an innovative way to resurrect previously effective resistance genes(Contreras et al.,2023),but it has been less effective at introducing new forms of disease resistance to crops.

关键词： breeding resistance editing

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Shedding light on neurons:optical approaches for neuromodulation

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National Science Review 2022年第10期9卷 34-54页

作者： Shan jiang Xiang Wu nicholas j.Rommelfanger Zihao Ou Guosong Hong Department of Materials Science and Engineering Stanford University Wu Tsai Neurosciences Institute Stanford University Department of Applied Physics Stanford University

Today’ s optical neuromodulation techniques are rapidly evolving,benefiting from advances in photonics,genetics and materials science.In this review,we provide an up-to-date overview of the latest optical approaches for neuromodulation.We begin with the physical principles and constraints underlying the interaction between light and neural tissue.We then present advances in optical neurotechnologies in seven modules:conventional optical fibers,multifunctional fibers,optical waveguides,light-emitting diodes,upconversion nanoparticles,optical neuromodulation based on the secondary effects of light,and unconventional light sources facilitated by ultrasound and magnetic fields.We conclude our review with an outlo ok on new methods and mechanisms that afford optical neuromodulation with minimal invasiveness and footprint.

关键词： optical neuromodulation optogenetics neural interfaces

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Prospective associations between joint categories of physical activity and insomnia symptoms with onset of poor mental health in a population-based cohort

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journal of Sport and Health Science 2023年第3期12卷 295-303页

作者： Mitch j Duncan Elizabeth G Holliday Nicola W Burton nicholas Glozier Stina Oftedal School of Medicine and Public Health College of HealthMedicineand WellbeingThe University of NewcastleCallaghanNSW 2308Australia Priority Research Centre for Physical Activity and Nutrition The University of NewcastleCallaghanNSW 2308Australia School of Applied Psychology Griffith UniversityBrisbaneQLD 4122Australia Menzies Health Institute Queensland Griffith UniversityBrisbaneQLD 4122Australia Brain and Mind Centre Central Clinical SchoolThe University of SydneyNSW 2050Australia

Background:Physical inactivity and insomnia symptoms are independently associated with increased risk of depression and anxiety;however,few studies jointly examine these risk factors.This study aimed to prospectively examine the joint association of physical activity(PA)and insomnia symptoms with onset of poor mental health in adults.Methods:Participants from the 2013 to 2018 annnual waves of the Household Income and Labour Dynamics in Australia panel study who had good mental health(Mental Health Inventory-5>54)in 2013,and who completed at least 1 follow-up survey(2014-2018),were included(n=10,977).Poor mental health(Mental Health Inventory-5≤54)was assessed annually.Baseline(2013)PA was classified as high/moderate/low,and insomnia symptoms(i.e.,trouble sleeping)were classified as no insomnia symptoms/insomnia symptoms,with 6 mutually exclusive PAinsomnia symptom groups derived.Associations of PA-insomnia symptom groups with onset of poor mental health were examined using discrete-time proportional-hazards logit-hazard models.Results:There were 2322 new cases of poor mental health(21.2%).Relative to the high PA/no insomnia symptoms group,there were higher odds(odds ratio and 95%confidence interval(95%CI))of poor mental health among the high PA/insomnia symptoms(OR=1.87,95%CI:1.57-2.23),moderate PA/insomnia symptoms(OR=1.93,95%CI:1.61-2.31),low PA/insomnia symptoms(OR=2.33,95%CI:1.96-2.78),and low PA/no insomnia symptoms(OR=1.14,95%CI:1.01-1.29)groups.Any level of PA combined with insomnia symptoms was associated with increased odds of poor mental health,with the odds increasing as PA decreased.Conclusion:The se findings highlight the potential benefit of interventions targeting both PA and insomnia symptoms for promoting mental health.

关键词： Depression Physical activity Sleep quality

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Role of c-Myc in lung cancer:Progress,challenges,and prospects

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Chinese Medical journal Pulmonary and Critical Care Medicine 2023年第3期1卷 129-138页

作者： nicholas j.Wallbillich Hua Lu Department of Biochemistry and Molecular Biology Tulane University School of Medicine1430 Tulane AvenueNew OrleansLA 70112USA Tulane Cancer Center Tulane University School of Medicine1700 Tulane AvenueNew OrleansLA 70112USA

Lung cancer remains the leading cause of cancer-related deaths worldwide.Despite the recent advances in cancer therapies,the 5-year survival of non-small cell lung cancer(NSCLC)patients hovers around 20%.Inherent and acquired resistance to therapies(including radiation,chemotherapies,targeted drugs,and combination therapies)has become a significant obstacle in the successful treatment of NSCLC.c-Myc,one of the critical oncoproteins,has been shown to be heavily associated with the malignant cancer phenotype,including rapid proliferation,metastasis,and chemoresistance across multiple cancer types.The c-Myc proto-oncogene is amplified in small cell lung cancers(SCLCs)and overexpressed in over 50%of NSCLCs.c-Myc is known to actively regulate the tran-scription of cancer stemness genes that are recognized as major contributors to tumor progression and therapeutic resistance;thus,targeting c-Myc either directly or indirectly in mitigation of the cancer stemness phenotype be-comes a promising approach for development of a new strategy against drug resistant lung cancers.This review will summarize what is currently known about the mechanisms underlying c-Myc regulation of cancer stemness and its involvement in drug resistance and offer an overview on the current progress and future prospects in therapeutically targeting c-Myc in both SCLC and NSCLC.

关键词： Cancer dormancy Cancer stem cells c-Myc Drug resistance Epidermal growth factor receptor Lung cancer Non-small cell lung cancer Small cell lung cancer

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Putting PLX5622 into perspective:microglia in central nervous system viral infection

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Neural Regeneration Research 2023年第6期18卷 1269-1270页

作者： Alanna G.Spiteri nicholas j.C.King Viral Immunopathology Laboratory InfectionImmunity and Inflammation Research ThemeSchool of Medical SciencesFaculty of Medicine and HealthThe University of SydneySydneyNSWAustralia Sydney Cytometry The University of Sydney and Centenary InstituteSydneyNSWAustralia Ramaciotti Facility for Human Systems Biology The University of Sydney and Centenary InstituteSydneyNSWAustralia Charles Perkins Centre The University of SydneyAustralia The University of Sydney Institute for Infectious Diseases The University of SydneySydneyNSWAustralia The University of Sydney Nano Institute the University of SydneySydneyNSWAustralia

Elucidating the exact contribution of microglia to central nervous system(CNS)pathology has historically been extremely challenging.These resident parenchymal myeloid cells are considered to have critical roles as frontline responders during pathogen invasion and CNS perturbation.Thus,understanding the precise temporal kinetics of microglial function is central to the evolution of novel therapeutics for disease intervention and/or resolution(Spiteri et al.,2022a).The development of PLX5622,a colony-stimulating factor 1 receptor(CSF-1R)inhibitor typically formulated into a rodent chow for simple oral administration has facilitated exploration of microglial functions in disease(Spangenberg et al.,2019).

关键词： invasion system precise

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Seasonal resource selection of an arboreal habitatspecialist in a human-dominated landscape: A case studyusing red panda

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Current Zoology 2023年第1期69卷 1-11页

作者： Damber Bista Greg S.Baxter nicholas j.Hudson Peter j.Murray School of Agriculture and Food Sciences(Wildlife Science Unit) The University of QueenslandGattonQLD 4343Australia School of Agriculture and Environmental Science University of Southern QueenslandDarling HeightsQLD 4350Australia

Human-dominated landscapes provide heterogeneous wildlife habitat. Conservation of habitat specialists, like red pandas Ailurus fulgens, inhabiting such landscapes is challenging. Therefore, information on resource use across spatial and temporal scales could enable informed-decisionmaking with better conservation outcomes. We aimed to examine the effect of geo-physical, vegetation, and disturbance variables on fine-scalehabitat selection of red pandas in one such landscape. We equipped 10 red pandas with GPS collars in eastern Nepal in 2019 and monitoredthem for 1 year. Our analysis was based on a generalized-linear-mixed model. We found the combined effect of geo-physical, vegetation, anddisturbance variables resulted in differences in resource selection of red pandas and that the degree of response to these variables variedacross seasons. Human disturbances, especially road and cattle herding activities, affected habitat utilization throughout the year whereas othervariables were important only during restricted periods. For instance, geo-physical variables were influential in the premating and cub-rearingseasons while vegetation variables were important in all seasons other than premating. Red pandas selected steeper slopes with high solarinsolation in the premating season while they occupied elevated areas and preferred specific aspects in the cub-rearing season. Furthermore,the utilized areas had tall bamboo in the birthing and cub-rearing seasons while they also preferred diverse tree species and high shrub coverin the latter. Our study demonstrates the significance of season-specific management, suggests the importance of specific types of vegetationduring biologically crucial periods, and emphasizes the necessity to minimize disturbances throughout the year.

关键词： Ailurus fulgens anthropogenic disturbances habitat specialists habitat utilization resource use spatio-temporal variation vegetation

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